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<div class="title">C:/Users/cmbruns/svn/moltk/c++/include/moltk/Biosequence.h</div>  </div>
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<a href="Biosequence_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00020"></a>00020 <span class="comment">*/</span>
<a name="l00021"></a>00021 
<a name="l00022"></a>00022 <span class="comment">/*</span>
<a name="l00023"></a>00023 <span class="comment"> * Biosequence.h</span>
<a name="l00024"></a>00024 <span class="comment"> *</span>
<a name="l00025"></a>00025 <span class="comment"> *  Created on: Oct 5, 2011</span>
<a name="l00026"></a>00026 <span class="comment"> *      Author: brunsc</span>
<a name="l00027"></a>00027 <span class="comment"> */</span>
<a name="l00028"></a>00028 
<a name="l00029"></a>00029 <span class="preprocessor">#ifndef BIOSEQUENCE_H_</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span><span class="preprocessor">#define BIOSEQUENCE_H_</span>
<a name="l00031"></a>00031 <span class="preprocessor"></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &quot;<a class="code" href="Printable_8h.html">moltk/Printable.h</a>&quot;</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00034"></a>00034 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00035"></a>00035 <span class="preprocessor">#include &lt;iterator&gt;</span>
<a name="l00036"></a>00036 
<a name="l00037"></a>00037 <span class="keyword">namespace </span>moltk
<a name="l00038"></a>00038 {
<a name="l00039"></a>00039 
<a name="l00040"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html">00040</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a>
<a name="l00041"></a>00041 {
<a name="l00042"></a>00042 <span class="keyword">public</span>:
<a name="l00043"></a>00043 
<a name="l00044"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">00044</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a>
<a name="l00045"></a>00045     {
<a name="l00046"></a>00046     <span class="keyword">public</span>:
<a name="l00047"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">00047</a>         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">BaseResidue</a>() {}
<a name="l00048"></a>00048         <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a77878b4ad45b49071fbd48bc013cb739">getOneLetterCode</a>() <span class="keyword">const</span> = 0;
<a name="l00049"></a>00049         <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#ab8bff99240309f8cda23b24ce7374961">getResidueNumber</a>() <span class="keyword">const</span> = 0;
<a name="l00050"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a988df56becfb00e5068c6b63b6625cde">00050</a>         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a988df56becfb00e5068c6b63b6625cde">operator char</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a77878b4ad45b49071fbd48bc013cb739">getOneLetterCode</a>();}
<a name="l00051"></a>00051 
<a name="l00052"></a>00052     <span class="keyword">private</span>:
<a name="l00053"></a>00053         <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aed773ae21d9267adcfebf533b38a2880">BaseResidue</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a>&amp;);
<a name="l00054"></a>00054     };
<a name="l00055"></a>00055 
<a name="l00056"></a>00056 
<a name="l00057"></a>00057     <span class="comment">// TODO - Does GapResidue belong somewhere else?  Biosequence or Alignment?</span>
<a name="l00059"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html">00059</a> <span class="comment"></span>    <span class="keyword">class </span><a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html" title="GapResidue is used in Alignments.">GapResidue</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a>
<a name="l00060"></a>00060     {
<a name="l00061"></a>00061     <span class="keyword">public</span>:
<a name="l00065"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a2f3a7c0c17dd557680b24e6bac20631b">00065</a>         <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a2f3a7c0c17dd557680b24e6bac20631b" title="GapResidue has the residue number of the preceding non-gap residue.">GapResidue</a>(<span class="keywordtype">int</span> residueNumberParam)
<a name="l00066"></a>00066             : <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a802e24f86c91fd64a57dc2d1270efa16">residueNumber</a>(residueNumberParam)
<a name="l00067"></a>00067         {}
<a name="l00068"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a107b6171cc497a21470922469f12fd73">00068</a>         <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a107b6171cc497a21470922469f12fd73">getOneLetterCode</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <span class="charliteral">&#39;-&#39;</span>;}
<a name="l00069"></a><a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a802e24f86c91fd64a57dc2d1270efa16">00069</a>         <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#abadd5c5253a8b940b82600f73e8440f6">getResidueNumber</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a802e24f86c91fd64a57dc2d1270efa16">residueNumber</a>;};
<a name="l00070"></a>00070 
<a name="l00071"></a>00071     <span class="keyword">protected</span>:
<a name="l00072"></a>00072         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1GapResidue.html#a802e24f86c91fd64a57dc2d1270efa16">residueNumber</a>;
<a name="l00073"></a>00073     };
<a name="l00074"></a>00074 
<a name="l00075"></a>00075 
<a name="l00076"></a>00076 <span class="keyword">public</span>:
<a name="l00077"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">00077</a>     <a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">BaseBiosequence</a>() {}
<a name="l00078"></a><a class="code" href="classmoltk_1_1BaseBiosequence.html#a50d0c5d8f88038a316eb2cf1a4a8cb54">00078</a>     <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#a50d0c5d8f88038a316eb2cf1a4a8cb54">~BaseBiosequence</a>() {}
<a name="l00079"></a>00079     <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#a814d3dd94202969806d797d8f176b27f">print_to_stream</a>(std::ostream&amp; os) <span class="keyword">const</span>;
<a name="l00080"></a>00080     <span class="keyword">virtual</span> <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html#a5dfd87e1a64a3cf2479142bede9baffd">getNumberOfResidues</a>() <span class="keyword">const</span> = 0;
<a name="l00081"></a>00081     <span class="keyword">virtual</span> <span class="keyword">const</span> BaseResidue&amp; <a class="code" href="classmoltk_1_1BaseBiosequence.html#a8bdac042503a95bbd2579bea43e0538a">getResidue</a>(<span class="keywordtype">size_t</span> index) <span class="keyword">const</span> = 0;
<a name="l00082"></a>00082 
<a name="l00083"></a>00083 <span class="keyword">private</span>:
<a name="l00084"></a>00084     <a class="code" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">BaseBiosequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a>&amp;);
<a name="l00085"></a>00085 };
<a name="l00086"></a>00086 
<a name="l00087"></a>00087 
<a name="l00088"></a><a class="code" href="classmoltk_1_1Biosequence.html">00088</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Biosequence.html">Biosequence</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a>
<a name="l00089"></a>00089 {
<a name="l00090"></a>00090 <span class="keyword">public</span>:
<a name="l00091"></a>00091 
<a name="l00092"></a>00092 
<a name="l00093"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html">00093</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html">Residue</a> : <span class="keyword">public</span> BaseResidue
<a name="l00094"></a>00094     {
<a name="l00095"></a>00095     <span class="keyword">public</span>:
<a name="l00096"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a93cd39aca44de2374449b7a24b103bba">00096</a>         <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a93cd39aca44de2374449b7a24b103bba">Residue</a>(<span class="keywordtype">char</span> oneLetterCodeParam, <span class="keywordtype">int</span> residueNumberParam)
<a name="l00097"></a>00097             : <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">oneLetterCode</a>(oneLetterCodeParam)
<a name="l00098"></a>00098             , <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">residueNumber</a>(residueNumberParam)
<a name="l00099"></a>00099         {}
<a name="l00100"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aca32fbbf78533e484553924eea0d24d8">00100</a>         <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a93cd39aca44de2374449b7a24b103bba">Residue</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html">Residue</a>&amp; rhs)
<a name="l00101"></a>00101             : <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">oneLetterCode</a>(rhs.<a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">oneLetterCode</a>)
<a name="l00102"></a>00102             , <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">residueNumber</a>(rhs.<a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">residueNumber</a>)
<a name="l00103"></a>00103         {}
<a name="l00104"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a7e005a11972aa041faa3f1f3702ab4eb">00104</a>         <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a7e005a11972aa041faa3f1f3702ab4eb">getOneLetterCode</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">oneLetterCode</a>;}
<a name="l00105"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a907f3ea3832e3743cac0cb35d37632e8">00105</a>         <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#a907f3ea3832e3743cac0cb35d37632e8">getResidueNumber</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">residueNumber</a>;}
<a name="l00106"></a>00106 
<a name="l00107"></a>00107     <span class="keyword">protected</span>:
<a name="l00108"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">00108</a>         <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aa0247adc645368ac84e5541c70f3bd3b">oneLetterCode</a>;
<a name="l00109"></a><a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">00109</a>         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html#aaf6b830867ef2d8c08463ed0291d4882">residueNumber</a>;
<a name="l00110"></a>00110     };
<a name="l00111"></a>00111 
<a name="l00112"></a>00112 
<a name="l00113"></a>00113     <span class="comment">// STL-conformant iterators</span>
<a name="l00114"></a><a class="code" href="classmoltk_1_1Biosequence.html#a73efd4ab87cb40f3fc1d8d85aae8fd45">00114</a>     <span class="keyword">typedef</span> std::vector&lt;Residue&gt; <a class="code" href="classmoltk_1_1Biosequence.html#a73efd4ab87cb40f3fc1d8d85aae8fd45">ResidueList</a>;
<a name="l00115"></a><a class="code" href="classmoltk_1_1Biosequence.html#aad7e1fe0d1a4f9fb0b7e8c6c760e2f4e">00115</a>     <span class="keyword">typedef</span> ResidueList::iterator <a class="code" href="classmoltk_1_1Biosequence.html#aad7e1fe0d1a4f9fb0b7e8c6c760e2f4e">iterator</a>;
<a name="l00116"></a><a class="code" href="classmoltk_1_1Biosequence.html#aebf58247788445ce907bd0a5af4d7e65">00116</a>     <span class="keyword">typedef</span> ResidueList::const_iterator <a class="code" href="classmoltk_1_1Biosequence.html#aebf58247788445ce907bd0a5af4d7e65">const_iterator</a>;
<a name="l00117"></a>00117 
<a name="l00118"></a>00118 <span class="keyword">public</span>:
<a name="l00119"></a><a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">00119</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>() {}
<a name="l00120"></a>00120     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> std::string&amp; str);
<a name="l00121"></a>00121     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> * str);
<a name="l00122"></a><a class="code" href="classmoltk_1_1Biosequence.html#a28917bc01df6b7d3fa995476b7258404">00122</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html">Biosequence</a>&amp; rhs)
<a name="l00123"></a>00123         : <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>(rhs.<a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>)
<a name="l00124"></a>00124     {}
<a name="l00125"></a><a class="code" href="classmoltk_1_1Biosequence.html#a2fe7b008000e37c494f64d720651b165">00125</a>     <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Biosequence.html#a2fe7b008000e37c494f64d720651b165">~Biosequence</a>() {}
<a name="l00126"></a><a class="code" href="classmoltk_1_1Biosequence.html#abad99e26e19c60af1af07199b2ce5d83">00126</a>     <span class="keyword">virtual</span> <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Biosequence.html#abad99e26e19c60af1af07199b2ce5d83">getNumberOfResidues</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.size();}
<a name="l00127"></a><a class="code" href="classmoltk_1_1Biosequence.html#aa47776dc3ccab6438598c34a3e801c8d">00127</a>     <span class="keyword">virtual</span> <span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#aa47776dc3ccab6438598c34a3e801c8d">getResidue</a>(<span class="keywordtype">size_t</span> index)<span class="keyword"> const </span>{
<a name="l00128"></a>00128         <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>[index];
<a name="l00129"></a>00129     }
<a name="l00130"></a><a class="code" href="classmoltk_1_1Biosequence.html#a46b8cff2776f32be22b1f8b789d5952f">00130</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aad7e1fe0d1a4f9fb0b7e8c6c760e2f4e">iterator</a> <a class="code" href="classmoltk_1_1Biosequence.html#a46b8cff2776f32be22b1f8b789d5952f">begin</a>() {<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.begin();}
<a name="l00131"></a><a class="code" href="classmoltk_1_1Biosequence.html#a36cc1fa00528fb51769b3b33169928e8">00131</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aebf58247788445ce907bd0a5af4d7e65">const_iterator</a> <a class="code" href="classmoltk_1_1Biosequence.html#a36cc1fa00528fb51769b3b33169928e8">begin</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.begin();}
<a name="l00132"></a><a class="code" href="classmoltk_1_1Biosequence.html#aa6bbd520b7bc5a34d35eedbcdc90322d">00132</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aad7e1fe0d1a4f9fb0b7e8c6c760e2f4e">iterator</a> <a class="code" href="classmoltk_1_1Biosequence.html#aa6bbd520b7bc5a34d35eedbcdc90322d">end</a>() {<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.end();}
<a name="l00133"></a><a class="code" href="classmoltk_1_1Biosequence.html#a4929eb2b4139ccd012420f981d0e2ce1">00133</a>     <a class="code" href="classmoltk_1_1Biosequence.html#aebf58247788445ce907bd0a5af4d7e65">const_iterator</a> <a class="code" href="classmoltk_1_1Biosequence.html#a4929eb2b4139ccd012420f981d0e2ce1">end</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.end();}
<a name="l00134"></a>00134 
<a name="l00135"></a><a class="code" href="classmoltk_1_1Biosequence.html#a66b15088a7c750db149b6f67c790ee90">00135</a>     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html">Residue</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a66b15088a7c750db149b6f67c790ee90">operator[]</a>(<span class="keywordtype">int</span> ix)<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>[ix];}
<a name="l00136"></a><a class="code" href="classmoltk_1_1Biosequence.html#a500e2c1d54c1238555aecef0c58a31d9">00136</a>     <a class="code" href="classmoltk_1_1Biosequence_1_1Residue.html">Residue</a>&amp; <a class="code" href="classmoltk_1_1Biosequence.html#a500e2c1d54c1238555aecef0c58a31d9">operator[]</a>(<span class="keywordtype">int</span> ix) {<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>[ix];}
<a name="l00137"></a><a class="code" href="classmoltk_1_1Biosequence.html#a1d0aaba080ec6433f5af7a4d182f1ffb">00137</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1d0aaba080ec6433f5af7a4d182f1ffb">size</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>.size();}
<a name="l00138"></a>00138 
<a name="l00139"></a>00139 <span class="keyword">protected</span>:
<a name="l00140"></a><a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">00140</a>     <a class="code" href="classmoltk_1_1Biosequence.html#a73efd4ab87cb40f3fc1d8d85aae8fd45">ResidueList</a> <a class="code" href="classmoltk_1_1Biosequence.html#a1c15a8e308e64576eabc23e08a7742f6">residues</a>;
<a name="l00141"></a>00141 };
<a name="l00142"></a>00142 
<a name="l00143"></a>00143 } <span class="comment">// namespace moltk</span>
<a name="l00144"></a>00144 
<a name="l00145"></a>00145 <span class="preprocessor">#endif </span><span class="comment">/* BIOSEQUENCE_H_ */</span>
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